Dice eggplant into 1/2-inch cubes and place in a colander in the sink and add the eggplant. Sprinkle with 2 teaspoon kosher salt and let sit for 15-20 minutes. This encourages the eggplant to sweat—pulling out some of the bitterness. After, rinse the eggplant and let it dry thoroughly.
Meanwhile, dice the zucchini, onion and tomato into 1/2-inch cubes and place it onto a baking sheet.
Once the eggplant is drained and dry, add it to the sheet pan with a drizzle of 1 tablespoon of olive oil. Roast in oven for 30 minutes.
Bring a medium pot of water to a boil. Add a pinch of salt. Cook pasta for 8-9 minutes.
Heat a large saute pan over medium heat, add the remaining two tablespoon of olive oil. Once hot, add in the crushed garlic cloves and crushed red pepper flakes. Let cook for 2 minutes until garlic starts to brown.
Pour in the tomato sauce, salt, pepper, Italian seasoning and thyme. Stir in the roasted vegetables and let cook for 5 minutes.
Toss in the cooked pasta and stir to coat. Cook for another 5 minutes to let flavors meld, then serve!